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<title>Generic Genome Browser</title>
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<h1>Generic Genome Browser, v2 (Cloud Image)</h1>

<a href="http://www.gmod.org/"><img src="gmod_cog.jpeg" border="0" align="RIGHT"></a>

<p>

Welcome to the Generic Genome Browser (Cloud Image)!

<h2>Documentation</h2>

<dl>
  <dt><b>Online tutorial and sample data files</b></dt>
  <dd><a href="tutorial/tutorial.html">/var/www/gbrowse2/tutorial<a>.</dd>
  <dt><b>Installation and configuration manual</b></dt>
  <dd><a href="http://gmod.org/wiki/GBrowse_2.0_HOWTO">GBrowse 2.0 HOWTO</a></dd>
  <dt><b>Example scripts to control GBrowse from the command line</b></dt>
  <dd><a href="example_scripts">/var/www/gbrowse2/example_scripts</a></dd>
</dl>

<h2>Starter Databases</h2>

<p>

A series of starter databases have been preconfigured for you, consisting of:

<ul>
<li><a href="/fgb2/gbrowse/sacCer3">S. cerevisiae genome (April 11, sacCer3), Genes and DNA only</a></li>
<li><a href="/fgb2/gbrowse/yeast_advanced">S. cerevisiae, Chromosomes 1+2, (more tracks)</a></li>
<li><a href="/fgb2/gbrowse/yeast_chado">S. cerevisiae, Chromosomes 1+2, (Chado database)</a></li>
<li><a href="/fgb2/gbrowse/ce10">C. elegans genome (WS220, ce10), Genes and DNA only</a></li>
<li><a href="/fgb2/gbrowse/hg19">H. sapiens genome (hg19, GRCh37), Genes and DNA only</a></li>
</ul>

<p>

You may add additional starter genomes at any time by running the
command line script gbrowse_import_ucsc.pl and providing
the <a href="genome.ucsc.edu">UCSC Genome Browser</a> build name:

<pre>
 gbrowse_import_ucsc.pl mm10 'M. musculus genome (mm10, GRCm38)' 
</pre>

<h2>Directory Paths</h2>

<p>

For future reference, here is where you've installed GBrowse's various
components:

<dl>
  <dt>GBrowse documentation, stylesheets and in-memory databases.
  <dd><b>$HTDOCS</b>
      <p>
  <dt>GBrowse configuration files
  <dd><b>$CONF</b>
      <p>
  <dt>Preinstalled sample database(s)
  <dd><b>$DATABASES</b>
      <p>
  <dt>GBrowse CGI (web) scripts
  <dd><ul>
          <li><b>$CGIBIN/gbrowse</b>
          <li><b>$CGIBIN/gbrowse_img</b>
          <li><b>$CGIBIN/gbrowse_details</b>
      </ul>
      <p>
  <dt>Temporary directories for cached images and sessions.
  <dd><b>$TMP</b>
</dl>

<p>

<h2>Learning More</h2>

<p>

To find out more about Gbrowse, try the:

<ul>
  <li><a href="http://gmod.org/wiki/GBrowse_2.0_HOWTO">GBrowse 2.0 HOWTO</a>
  <li><a href="tutorial/tutorial.html">GBrowse Tutorial</a>
 <!-- <li><a href="contrib/conf_files">Sample Configuration Files</a> -->
</ul>


<hr>
<address>Lincoln D. Stein, lstein@cshl.org<br>
<a href="http://www.cshl.org/">Cold Spring Harbor Laboratory</a></address>
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Last modified: Thu Mar 18 18:59:16 PDT 2010
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